How do I install the pdb mcp server?

Use a recorded configuration for your client, replace example credential values and paths, and verify the documented runtime. Restart or reconnect the client, then inspect the available tools.

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PDB MCP Server

A comprehensive Model Context Protocol server for accessing Protein Data Bank (PDB) with 28 structural biology tools for protein structure analysis

Local serverstdio

What is the PDB MCP Server?

A comprehensive Model Context Protocol server for accessing Protein Data Bank (PDB) with 28 structural biology tools for protein structure analysis, validation, and

The short version

A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.

More MCP options

Compare MCP servers by category, or browse hosted MCP servers if you prefer an endpoint over a local process.

Recorded tools

Check the linked publisher documentation and your connected client's tool list. Names and availability can vary with the server version and account permissions.

Tool	What it does
search_structures	Search PDB database for protein structures by keyword, protein name, or PDB ID
get_structure_info	Get detailed information for a specific PDB structure
download_structure	Download structure coordinates in various formats (PDB, mmCIF, mmTF, XML)
search_by_uniprot	Find PDB structures associated with a UniProt accession
get_structure_quality	Get structure quality metrics and validation data

How to install the PDB MCP Server

{
  "mcpServers": {
    "pdb-server": {
      "command": "node",
      "args": [
        "/path/to/pdb-server/build/index.js"
      ]
    }
  }
}

From the project documentation. Replace placeholders and example paths before connecting.

Example prompts to try

“Use PDB to search structures.”
“Use PDB to get structure info.”
“Use PDB to download structure.”

Frequently asked questions

A comprehensive Model Context Protocol server for accessing Protein Data Bank (PDB) with 28 structural biology tools for protein structure analysis, validation, and Confirm the tools offered by your installed version in the connected client. Tool availability and permissions depend on the server and account configuration.